As the human project shifts into production sequencing, a plan is developing for sequencing the mouse genome. The current plan employs a "sequence first, map second" strategy which, like the human project, is based on shotgun sequencing of BAC clones comprising contiguous regions of the genome of the selected mouse strain (C57BL6/J). Libraries constructed in bacterial artificial chromosomes (BAC) vectors have become the choice for high throughput genomic sequencing projects because of their cloning capacity and high stability. The current whole-genome approach, which has been validated in the human genome sequencing project, uses BAC end sequences and restriction fingerprints to build BAC contigs. Restriction fingerprints not only serve as independent confirmation of BAC contigs assembled based on BAC end sequence, but also enable identification of chimeric BACs and clones with internal deletions. This map-as-you-go strategy saves substantial time and effort in constructing sequence ready maps. This proposal is to perform BAC end sequencing at TIGR and restriction fingerprinting at the Clemson University Genomics Institute Physical Mapping Center from the mouse BAC library or libraries constructed to support mouse genome sequencing. The clones, the sequences, gel images of the fingerprints, and the binning of the clones using the FPC program (C. Soderlund, Sanger Centre) will be an available resource for those sequencing the mouse genome, and the community at large. We will continue our focus on quality in this BAC clone end sequencing and restriction fingerprinting project while developing and implementing automation and new methodologies for reducing costs and increasing throughput.